4EXM | pdb_00004exm

The crystal structure of an engineered phage lysin containing the binding domain of pesticin and the killing domain of T4-lysozyme

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Pesticin receptor binding domain-like	8092867	3002635	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Lysozyme-like	8033861	3001879	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Lysozyme-like	8033861	3001879	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Pesticin receptor binding domain-like	8092867	3002635	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Lysozyme-like	8033861	3001879	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pesticin receptor binding domain-like	8092867	3002635	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Pesticin receptor binding domain-like	8092867	3002635	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lysozyme-like	8033861	3001879	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	TPR_COPA_B	e4exmD1	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: TPR_COPA_B	ECOD (v294.1)
C	VHP	e4exmC1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Notch heterodimerization domain	T: Notch heterodimerization domain	F: VHP	ECOD (v294.1)
B	SHMT	e4exmB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: SHMT	ECOD (v294.1)
B		e4exmB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F:	ECOD (v294.1)
A	Docking	e4exmA1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Docking	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.530.40	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
C	1.10.530.40	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
B	1.10.530.40	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
A	1.10.530.40	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00959	Phage lysozyme (Phage_lysozyme)	Phage lysozyme	This family includes lambda phage lysozyme and E. coli endolysin.	Domain
A, B, C, D	PF21613	Pesticin, receptor binding domain (Pesticin_RB)	Pesticin, receptor binding domain	This domain is found at the N-terminal end of Pesticin from Yersinia pestis (Pst). Pst is a toxin that kills related bacteria of the same niche as Y.pestis. It is organised into three domains: an N-terminal translocation domain, the intermediate rece ...	This domain is found at the N-terminal end of Pesticin from Yersinia pestis (Pst). Pst is a toxin that kills related bacteria of the same niche as Y.pestis. It is organised into three domains: an N-terminal translocation domain, the intermediate receptor binding domain (RB, this entry), and a C-terminal activity domain (Pfam:PF16754). This domain shows a beta-sheet of seven anti-parallel beta-strands together with three helices. It is essential for the intimate contact with the outer membrane protein receptor [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Pesticin, Lysozyme Chimera	hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity	defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process cellular process macromolecule metabolic process symbiont-mediated cytolysis of host cell viral life cycle disruption of cell in another organism cytolysis biological process involved in interaction with host biological process involved in symbiotic interaction viral release from host cell by cytolysis exit from host cell viral process cytolysis in another organism viral release from host cell disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing cell wall organization or biogenesis cell wall macromolecule catabolic process cell wall macromolecule metabolic process	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR052619	Bacteriophage lysozyme-like	Family
A, B, C, D	IPR001165	T4-type lysozyme	Family
A, B, C, D	IPR034690	Endolysin T4 type	Family
A, B, C, D	IPR002196	Glycoside hydrolase, family 24	Family
A, B, C, D	IPR023347	Lysozyme domain superfamily	Homologous Superfamily
A, B, C, D	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR033791	Pesticin, translocation and receptor binding domain	Domain
A, B, C, D	IPR031922	Pesticin, C-terminal	Domain
A, B, C, D	IPR023347	Lysozyme domain superfamily	Homologous Superfamily
A, B, C, D	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.